Stem cell transcriptional networks : methods and protocols / edited by Benjamin L. Kidder. -- 2nd ed. -- New York : Humana Press, 2020. – (58.17/M592/v.2117)

Contents

Preface

Contributors

PART I  NEXT-GENERATION SEQUENCING TECHNOLOGIES AND DATA ANALYSIS

1  Epitope Tagging ChIP-Seq of DNA Binding Proteins Using CETCh-Seq

2  User-Friendly and Interactive Analysis of ChIP-Seq Data Using EaSeq

3  Evaluation of 3D Chromatin Interactions Using Hi-C

4  MSTD for Detecting Topological Domains from 3D Genomic Maps..

5  Creating 2D Occupancy Plots Using plot2DO

6  Detection of Epigenetic Field Defects Using a Weighted Epigenetic Distance-Based Method

PART II  ANALYSIS AND VISUALIZATION OF SINGLE-CELL AND BULK RNA-SEQ TRANSCRIPTOME DATA

7  Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx

8  Visualization of Single Cell RNA-Seq Data Using t-SNE in R

9  Use of SuperCT for Enhanced Characterization of Single-Cell Transcriptomic Profiles

10  Interactive Alternative Splicing Analysis of Human Stem Cells Using psichomics

11  Gene Ontology Semantic Similarity Analysis Using GOSemSim

PART III  DERIVATION OF STEM CELLS

12  Derivation of Maternal Epiblast Stem Cells from Haploid Embryos

13  Derivation of LIF-Independent Embryonic Stem Cells Using Inducible OCT4 Expression

14  Simultaneous Derivation of Embryonic and Trophoblast Stem Cells from Mouse Blastocysts

PART IV  TRANSCRIPTIONAL PROGRAMS THAT PROMOTE REPROGRAMMING, TRANSDIFFERENTIATION, AND CANCER FORMATION

15  Reprogramming Fibroblasts to Neural Stem Cells by Overexpression of the Transcription Factor Ptfla

16  Reprogramming of Fibroblasts to Neural Stem Cells by a Chemical Cocktail

17  Efficient RNA-Based Reprogramming of Disease-Associated Primary Human Fibroblasts into Induced Pluripotent Stem Cells

18  Direct Reprogramming of Mouse Embryonic Fibroblasts to Induced Trophoblast Stem Cells

19  Characterization of Arsenic-Induced Cancer Stem-Like Cells

Index